Preferences: Images

Open

Enable smart optimize for images with low signal: When enabled (checked), image display is automatically optimized if low signal is detected when opening files. Note that, if you're opening multiple image files, you can cancel the smart optimize operation by hitting the ESC key on your keyboard and choosing to cancel when prompted.

Zoom to fit on load:

  • When enabled (checked), the image and/or tracing is automatically sized to fill the window while preserving the aspect ratio.

    • With manually placed reference point: The top left corner of any opened image is placed at the top left corner of the viewing area regardless of where the reference point is. The image will then be centered and resized to fill as much of the viewing area as possible.

    • No reference point: The top left corner of the first opened image is placed in the top left corner of the viewing area and the reference point is automatically placed at the top left corner of the image. The image is then centered and resized to fill as much of viewing area as possible. The reference point will also move and remain aligned with the top left corner of image. The top left corner of the second opened image will also be placed at the top left corner of the viewing area, then be centered and resized. However, since the reference point was no longer in the top left corner of the viewing area, the top left corner of the second image will not be aligned with the reference point. This will be the case for all subsequently opened images.

  • When disabled (unchecked), the image and/or tracing is displayed using the reference point as the origin.

    • With manually placed reference point: The top left corner of any opened image will be placed at the top left corner of the viewing area regardless of where the reference point is located.

    • No reference point: The top left corner of the first opened image is placed at top left corner of viewing area and the reference point is automatically placed at the top left corner of the image. All subsequent images will be placed at top left corner of the viewing area regardless of where the reference point is located.

The reference point is the origin (0,0,0) of a data file. Each data file contains a single reference point and tracing data are calculated and saved relative to the reference point. The reference point is essential for maintaining accurate alignment of a data file and its corresponding experimental sample when collecting data over multiple sessions with a live camera feed.

Note that if opening a data file with existing images and/or tracings, they will be placed in the same location relative to the reference point as they were when the file was last open.

Load all stacks at same Z: If left unchecked, image stacks are loaded with the first image at the current Z position, with the images in the stack placed at regular intervals in Z compared to the first image. Check the box to load all image stacks at the same Z position.

Show Image Scaling dialog on opening image: By default, Neurolucida displays the Image Scaling dialog only when it cannot identify scaling. Check the box to display the dialog every time you open an image. This may be useful when:

  • You want to create

  • Images have been saved with inaccurate image scaling.

Enable resampling quality bias: This is an advanced feature that we recommend keeping disabled (unchecked) for the most part. Our Technical Services staff may recommend enabling it to increase the quality of image-data display. Enabling resampling quality bias, however, will decrease the speed of image loading.

View

Marquee around current image: Useful to identify the current image.

Alternative method: Use the Image Organizer; the current image is identified by a blue highlight for the image information.

Show images in Where Is mode: When checked, the acquired and imported image thumbnails are shown in their appropriate locations in Where Is mode.

Use image averaging: Acquires "n" images and averages these "n" acquisitions into a single image. Use this option if your camera generates a lot of noise in the image.

Number of images to use: Start with a small number and gradually increase until the noise reduction is satisfactory.

Reader Channel Colors: Displays the Image File Reader Channel Colors dialog box.

Use with multichannel image files that don't contain color specifications (e.g., Nikon IDS/ICS files) to assign colors to display.

Save

Save images when they are acquired: Select to automatically save the acquired images to a defined path.

Optional: Use a base name. As each image is saved, the program uses the base name and a number that increments by 1.

Suppress warning for saving single image of a stack There are two image save options in the file menu, Save/ Save as image and Save/ Save as image stack . If save image is chosen, but an image stack, rather than a single-plane image is the active file, you will see a warning that continuing will save just the current plane of the image stack. Select this option to suppress the warning.

When writing image files, write MBF-specific data to external XMP file: Select to create an external XMP file when saving an image. This will modify the original image and also save scaling and display adjustment information to an external XMP file where you can easily view and edit the image specific metadata.

When saving only image display adjustments, write these adjustments to just the external XMP file so the image file is not modified: Use this option to save changes to an external XMP file only. No changes will be made to the original image file.

Note that if the XMP file is present in the same folder as the image, Neurolucida will use the metadata contained in the XMP file when opening the image. If the XMP file is removed from the folder containing the image, Neurolucida will use the metadata that is embedded in the image file.

Clean temporary files on save failure: When saving JPX stacks, temporary JP2 files for each image plane are created. By default, those temporary files are deleted regardless of whether the save succeeds or fails. Select this option to keep the temporary files if the save fails.

Enable image organizer metadata editing: Select to enable the ability to edit metadata directly in the Image organizer window.

Luminance

Save extended component data: (relevant primarily for brightfield images) Check to save data about the RGB components of the image.

Aspect ratio

After zoom operation...: Sometimes the shapes of objects displayed on the monitor don’t seem to be an accurate representation of their actual (or expected) shapes. The perceived inaccuracy depends on how much the aspect ratio of the image file varies from the aspect ratio of the display monitor.

  • Image: For most images, the option to use aspect ratio of currently selected Image results in a satisfactory representation of the objects. This is because the aspect ratio of the pixels in the image file and the aspect ratio of the pixels in the display monitor are very similar.

  • Lens: If there is a significant difference between the aspect ratio of the pixels in the image file and the aspect ratio of the pixels of the display monitor, the option to use aspect ratio of currently selected Image results in an image with seemingly distorted (stretched or compacted) objects in one dimension, for example with MRI images.

    To resolve the apparent image distortion, use the option to use aspect ratio of currently selected lens. If needed, create a software lens that matches the aspect ratio of your display (likely to be close to 1.0).

All measurements reported by the program are correct regardless of the option selected (and even if the image appears distorted) .